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3dpr

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{{Seed}}
 
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[[Image:3dpr.png|left|200px]]
 
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<!--
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==Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3==
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The line below this paragraph, containing "STRUCTURE_3dpr", creates the "Structure Box" on the page.
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<StructureSection load='3dpr' size='340' side='right'caption='[[3dpr]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3dpr]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human] and [https://en.wikipedia.org/wiki/Human_rhinovirus_2 Human rhinovirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPR FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DAO:LAURIC+ACID'>DAO</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpr OCA], [https://pdbe.org/3dpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpr RCSB], [https://www.ebi.ac.uk/pdbsum/3dpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpr ProSAT]</span></td></tr>
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{{STRUCTURE_3dpr| PDB=3dpr | SCENE= }}
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</table>
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== Disease ==
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[[https://www.uniprot.org/uniprot/VLDLR_HUMAN VLDLR_HUMAN]] Defects in VLDLR are the cause of cerebellar ataxia mental retardation and dysequilibrium syndrome type 1 (CMARQ1) [MIM:[https://omim.org/entry/224050 224050]]; also known as dysequilibrium syndrome (DES) or non-progressive cerebellar disorder with mental retardation. CMARQ1 is a congenital, non-progressive cerebellar ataxia associated with disturbed equilibrium, delayed ambulation, mental retardation and cerebellar hypoplasia. Additional features include short stature, strabismus, pes planus and, rarely, seizures.<ref>PMID:16080122</ref>
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== Function ==
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[[https://www.uniprot.org/uniprot/POLG_HRV2 POLG_HRV2]] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with human VLDLR to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-mediated endocytosis. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm.<ref>PMID:11034318</ref> <ref>PMID:12191477</ref> VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:11034318</ref> <ref>PMID:12191477</ref> Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription.<ref>PMID:11034318</ref> <ref>PMID:12191477</ref> Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:11034318</ref> <ref>PMID:12191477</ref> Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).<ref>PMID:11034318</ref> <ref>PMID:12191477</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).<ref>PMID:11034318</ref> <ref>PMID:12191477</ref> Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).<ref>PMID:11034318</ref> <ref>PMID:12191477</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:11034318</ref> <ref>PMID:12191477</ref> [[https://www.uniprot.org/uniprot/VLDLR_HUMAN VLDLR_HUMAN]] Binds VLDL and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. Binding to Reelin induces tyrosine phosphorylation of Dab1 and modulation of Tau phosphorylation (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dpr_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dpr ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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X-ray structures of human rhinovirus 2 (HRV2) in complex with soluble very-low-density lipoprotein receptors encompassing modules 1, 2, and 3 (V123) and five V3 modules arranged in tandem (V33333) demonstrates multi-modular binding around the virion's five-fold axes. Occupancy was 60% for V123 and 100% for V33333 explaining the high-avidity of the interaction. Surface potentials of 3D-models of all minor group HRVs and K-type major group HRVs were compared; hydrophobic interactions between a conserved lysine in the viruses and a tryptophan in the receptor modules together with coulombic attraction via diffuse opposite surface potentials determine minor group HRV receptor specificity.
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===Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3===
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Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition.,Querol-Audi J, Konecsni T, Pous J, Carugo O, Fita I, Verdaguer N, Blaas D FEBS Lett. 2009 Jan 5;583(1):235-40. Epub 2008 Dec 13. PMID:19073182<ref>PMID:19073182</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3dpr" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19073182}}, adds the Publication Abstract to the page
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*[[Human rhinovirus|Human rhinovirus]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19073182 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19073182}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Human]]
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3DPR is a 5 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_rhinovirus_2 Human rhinovirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPR OCA].
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==Reference==
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<ref group="xtra">PMID:19073182</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
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[[Category: Human rhinovirus 2]]
[[Category: Human rhinovirus 2]]
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[[Category: Fita, I.]]
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[[Category: Large Structures]]
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[[Category: Pous, J.]]
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[[Category: Fita, I]]
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[[Category: Querol-Audi, J.]]
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[[Category: Pous, J]]
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[[Category: Verdaguer, N.]]
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[[Category: Querol-Audi, J]]
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[[Category: Alternative splicing]]
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[[Category: Verdaguer, N]]
[[Category: Atp-binding]]
[[Category: Atp-binding]]
[[Category: Capsid protein]]
[[Category: Capsid protein]]
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[[Category: Coated pit]]
[[Category: Coated pit]]
[[Category: Covalent protein-rna linkage]]
[[Category: Covalent protein-rna linkage]]
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[[Category: Cytoplasm]]
 
[[Category: Cytoplasmic vesicle]]
[[Category: Cytoplasmic vesicle]]
[[Category: Egf-like domain]]
[[Category: Egf-like domain]]
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[[Category: Nucleotidyltransferase]]
[[Category: Nucleotidyltransferase]]
[[Category: Phosphoprotein]]
[[Category: Phosphoprotein]]
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[[Category: Polymorphism]]
 
[[Category: Protease]]
[[Category: Protease]]
[[Category: Receptor]]
[[Category: Receptor]]
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[[Category: Transport]]
[[Category: Transport]]
[[Category: Virion]]
[[Category: Virion]]
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[[Category: Virus]]
[[Category: Virus-protein complex]]
[[Category: Virus-protein complex]]
[[Category: Vldl]]
[[Category: Vldl]]
[[Category: Vldl-receptor]]
[[Category: Vldl-receptor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 10:50:38 2009''
 

Current revision

Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3

PDB ID 3dpr

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